Surface area of SUMA ROI

amehta · May 21, 2020, 8:31pm

Hi,

Is there a way to calculate the surface area of ROIs drawn in SUMA? SurfMeasures seems like the appropriate program, but I’m not sure how to process the SUMA ROI into the input spec file.

Thanks in advance.

dglen · May 22, 2020, 12:02am

Given an ROI on the surface made in SUMA, you first convert that to dataset that covers the whole surface with ROI2dataset (changing the pad_to_node option for the number of nodes in your surface minus 1). Choose the surface to apply the region. Then you can use the info_area option as a summary over all the surface or sum them over the nodes yourself with 3dBrickStat.

ROI2dataset -prefix testroi1 -pad_to_node 198811 -input testroi1.niml.roi
SurfMeasures -info_area -func n_area_A -spec std.141.FT_lh.spec -surf_A pial -cmask ‘-a testroi1.niml.dset -expr step(a)’ -out testsm.niml.dset
++ Notice SUMA_LoadSpec_eng (SUMA_Load_Surface_Object.c:4297 @19:44:34):
Label dsets should only be attached to
surfaces with LocalDomainParent = SAME).
LabelDset ././std.141.lh.aparc.a2009s.annot.niml.dset is ignored.

– total area 0 = 815.8
– from cmask, nodes skipped = 196773

3dBrickStat -sum testsm.niml.dset’[1]’
815.805

amehta · May 26, 2020, 3:33pm

Thanks for your quick response, Daniel.

I think I’m doing something wrong, because my dset file is a bunch of random characters (see screenshot attached) and 3dBrick Stat is giving me the following error:
(base) ashamehta-mbp:mri_ODP663 ashamehta$ 3dBrickStat -sum test.niml.dset’[1]’
** ERROR: selector index 1 is out of range 0…0
** ERROR: bad sub-brick selector [1]
** FATAL ERROR: Can’t open dataset ‘test.niml.dset[1]’
** Program compile date = Feb 26 2020

Here are the steps I took:

I converted the ROI to a dataset using:
ROI2dataset -prefix test -pad_to_node 139750 -input func_motor/stats_motor_ODP663_2020-02-27/test.niml.roi
I used the Surface Properties section of the Object Controller to find the number of nodes.
When using SurfMeasures to calculate area, I received the following error:

(base) ashamehta-mbp:mri_ODP663 ashamehta$ SurfMeasures -info_area -func n_area_A -spec struct/freesurfer_ODP663/SUMA/ODP663_both.spec -surf_A struct/freesurfer_ODP663/SUMA/lh.smoothwm.gii -cmask ‘-a test.niml.dset -expr step(a)’ -out test_surf_measure.niml.dset
** cmask and node list lengths differ (139751, 139750)

I then subtracted 1 from the number of nodes and tried:
ROI2dataset -prefix test -pad_to_node 139749 -input func_motor/stats_motor_ODP663_2020-02-27/test.niml.roi

This produced a dset file that I found the area of using SurfMeasures:
(base) ashamehta-mbp:mri_ODP663 ashamehta$ SurfMeasures -info_area -func n_area_A -spec struct/freesurfer_ODP663/SUMA/ODP663_both.spec -surf_A struct/freesurfer_ODP663/SUMA/lh.smoothwm.gii -cmask ‘-a test.niml.dset -expr step(a)’ -out test_surf_measure.niml.dset

– total area 0 = 15.4
– from cmask, nodes skipped = 139726

In case this is helpful, the output of 3dBrickStat without the selector index is:
(base) ashamehta-mbp:mri_ODP663 ashamehta$ 3dBrickStat -sum test.niml.dset
24

Do you spot the issue?
Thanks.

amehta · June 1, 2020, 3:47pm

Hi - wanted to follow up here to check if there’s a solution for this. Thanks!

dglen · June 2, 2020, 1:23am

It seems to me the second one was producing a useful result (15.4) and used the correct syntax with the number of nodes-1.

amehta · June 2, 2020, 6:18pm

Ok thank you! What is the best way to find the length of the node list of the spec file for SurfMeasures?

dglen · June 2, 2020, 7:50pm

If you want to find the number of nodes in a surface, you can use :

SurfInfo -N_Node -spec my.spec -surf_A surfname
N_Node=198812

where “my.spec” would be the name of the spec file you are interested in, and surfname is the name of the surface (like pial, wm, smoothwm,…).

If you want to find the number of nodes listed in a niml.dset or functional gifti dataset file, you can use:

3dinfo -ni ~/schaefer_yeo/MNI_N27/my.niml.dset
198812

amehta · June 2, 2020, 10:12pm

Thanks. And last question - why do I need to subtract 1 from the number of nodes when I convert the ROI to a dataset in order to match the number of nodes in the spec file for SurfMeasures?

dglen · June 2, 2020, 10:26pm

In AFNI, most things are counted from zero, so the last item with n elements is n-1. The ROIs are stored in a sparse format that many AFNI programs can not read directly. To be able to use it, convert the data to one that matches all the nodes of the surface from node 0 to node n-1.

amehta · June 2, 2020, 10:57pm

Got it, thanks so much for your help!